Moyes, the youngest manager in the premier league, was presented with the award by England boss Sven-Goran Eriksson on Monday at a League Managers' Association dinner.
It came just a few hours after the two men had a public dispute over the fitness and availability of Everton's teenage striker Wayne Rooney for England's friendly in South Africa.
Moyes left Preston North End to take over at Everton from Walter Smith in March last year. In his first full season he led them to seventh place, their best finish since 1996 and a huge improvement from last year's 15th.
Moyes, however, said he ended the season disappointed after Sunday's 2-1 home defeat by Manchester United saw Everton slip to seventh to miss out on a UEFA Cup place.
"I'm delighted and surprised to win the award," he said. "The disappointment we have suffered is immeasurable.
"Football is about taking opportunities when they come and we had a great opportunity this season.
"But when things die down, then hopefully we will realise what a good season it has been."
Manchester United boss Alex Ferguson won a separate award as premier league manager of the year and another as manager of the "decade" -- the league's first 10 years.
The first division manager of the year award was won by Harry Redknapp, who guided Portsmouth to the title in his first full season at Fratton Park.
Paul Jewell won the second division award after leading Wigan to the title with 100 points, losing just four games, while Wrexham's Denis Smith won the third division honours.
